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Chem@York Core 2&3 > Core 3: Biological Chemistry > Flashcards

Core 3: Biological Chemistry Flashcards

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1
Q

What are the four DNA base names? What is the RNA base? How are they classified into two groups?

A

There are two purines: Adenine and Guanine

There are three pyrimidines: Thymine, Cytosine and Uracil (RNA equivalent of T)

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2
Q

What is the name for three bases which code amino acids?

A

A codon.

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3
Q

What are the three main building blocks for DNA?

A

Phosphate esters(PO4R22-), carbohydrates (ribose and deoxyribose) and the organic bases.

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4
Q

Draw the linkage of the nucleotide. From where are the carbons labelled? In what direction does the chain assemble?

A

The carbon attached to the base is 1’. Assembled from 5’→3’

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5
Q

Which bases are complementry and how are they complimentary? How do the strands of DNA run in the double helix?

A

A-T and G-C have complimentary hydrogen bonding. The strands run anti-parallel, the direction of 5’ to 3’ run opposite directions.

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6
Q

What is misleading about the name nucleic acids and organic bases? What does this mean for the overall charge of DNA?

A

The acid, the phosphate ester, has already been deprotonated and the bases are very weak bases, millions of times weaker than NEt3. This gives DNA an overall negative charge.

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7
Q

What are the two molecular differences and the one macromolecular difference between DNA and RNA?

A

Molecular: 1. DNA has 2’-deoxyribose as its carbohydrate, RNA has ribose. Meaning RNA has an extra -OH.

  1. DNA uses Thymine as a base which has a methyl group that Uracil, the base used in RNA, lacks.

Macromolecular: DNA is double stranded whereas RNA is single stranded (can formed double strands but doesn’t typically).

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8
Q

Draw the mechanism for the change of cytosine to uracil. How fast is this mechanism?

A

The rate is slow but appreciable.

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9
Q

What is the structural difference between Thymine and Uracil?

A

Thymine has a methyl group which uracil is missing.

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10
Q

Draw the mechanism illustrating how RNA is more chemically reactive than DNA.

A
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11
Q

Which base paring is the strongest?

A

GC is stronger than AT

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12
Q

What enzyme is the synthesis of DNA perfomed by?

A

DNA polymerase

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13
Q

Why do viruses mutate rapidally?

A

They have to have enzymes that work faster than human enzymes to exploit human replication at the cost of specifity so changes are likely.

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14
Q

How are DNA base sequences determined?

A

Fluorophores are added to the bases, these are different for each base. The chains are broken up and seperated based on size by capillarly electrophoresis. This means the chains coming through the end to the capillary get slowly longer. The end bases are marked by the fluorophore and detected using a laser.

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15
Q

How does UV radiation damage DNA? How is this repaired and prevented?

A

Excited bases can react with other bases to form crosslinked DNA which causes mutation. DNA photolyase is activated by the same UV rays that damage the bases and reverses the process. Suncream contains chemicals that absorb the same wavelengths as those that mutate our DNA.

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16
Q

For cancer treatment we want to stop DNA synthesis, briefly describe four ways can this be done?

A
  1. Ribose can be converted to deoxyribose
  2. The 5’ phosphate can be removed
  3. Methyl groups can be added to uracil to convert it to thymine
  4. Adding fluorine to reactive sites such as the uracil site where methyl might be removes reactivity.
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17
Q

What is the role of lipids in cells?

A

They form the lipid bilayer which is a membrane which incases the cell and provides structure, selective transport and communication to the cell.

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18
Q

Name three types of lipid?

A
  1. Fatty acyl esters (phospholipids, glycolipids)
  2. Steriods (cholesterol)
  3. Waxes
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19
Q

What is the struture of phospholipids?

A

Two fatty acyl chains with ester links are attached to the platform - glycerol. Also attached to glycerol is a phosphate which has ester links to a polar alcohol.

This is shortened to a polar head group with two hydrophobic, greasy tails.

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20
Q

How would chemists convert a fatty acid to an ester? How does nature do the same?

A

Chemists could either directly react the acid with the alcohol in an equlibrium or convert the acid to an acyl chloride using SOCl2.

Nature uses a -SCoA or Co enzyme A group which is natures good leaving group.

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21
Q

What are the three driving forces for bilayer formation?

A
  1. Removes acyl chains from interfering with hydrogen bonding in the water.
  2. Van der Waals forces between the acyl chains when they are close.
  3. Polar head group interactions (electrostatic, hydrogen bonding).
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22
Q

What are the two types of membrane protein?

A

Integral and peripheral.

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23
Q

What is the structure of glycolipids? Where do these reside?

A

It has one fatty acyl chain attached to a different platform, sphingosine which is then attached to glucose or galactose as its head group. They are found on cell membranes to maintain their stability.

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24
Q

What type of lipid is cholesterol and what role does it serve in the cell membrane?

A

It disrupts the packing of the membrane lipids so increase fluidity, this is also done by unsaturated acyl chains.

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25
Q

What are the other names for carbohydrates? How can they be further classified?

A

Sugars and saccharides are both the same as carbohydrates.

Monosaccharides - one sugar unit

Disaccharide - two linked sugars

Oligosaccharide - three to 10 length sugar chain

Polysaccharide - >10 length sugar chain

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26
Q

How are D and L sugars classified?

A

D-glyceraldehyde has an -OH group to the right of the structure. All sugars that have matching stereochemistry on the highest number stereocentre are D.

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27
Q

What is the structure of glucose?

A
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28
Q

What is the actual name of a pyranose ring and which groups react? What is the stereochemical outcome?

A

A cyclic hemiacetal. The highest numbered stereocentre attacks the aldehyde group. Two possible isomers are possible, called the α and β anomers.

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29
Q

What is notable about the structure of glucose in ring form?

A

All stereocentres are equatorial. The anomeric carbon can change between both, in the β form it is in the equatiorial position.

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30
Q

Draw the three different ways of representing β-glucose and name them.

A

Fischer, Haworth and chair/flying wedge.

31
Q

How can you draw the Haworth projection from the Fischer projection?

A

All left facing groups on the Fischer form are up on the Haworth form, equivalently all right groups are down.

32
Q

Draw the mechanism for mutarotation.

A
33
Q

How are disaccharides linked?

A

Via an ester bond typically between carbons 1 and 4 in either the α or β position.

34
Q

How is the structure of GlcNAc different to that of glucose?

A

The -OH in the 2 position on the carbon ring is replaced by a -NHC(=O)CH3 group.

35
Q

What is an epimer?

A

A diastereoisomer of a sugar

36
Q

What epimer of glucose is galactose?

A

The 4-epimer

37
Q

How are peptide bonds formed by chemists and by nature?

A

Chemists would typically use an acyl chloride or DCC (an activated ester, lots of stability). In nature tRNA is used. The reaction is a condensation reaction that forms an amide bond.

38
Q

Briefly describe the four levels of protein structure.

A

Primary: The linear sequence of amino acids.

Secondary: The local areas of organsiation of the amino acid chain into β-sheets and α-helixes.

Tertiary: The view of the whole amino acid chain and how each region of organisation arranges together in space.

Quaternary: When proteins dimerise and join together in other ways such as clipping together.

39
Q

Over how many amino acids is a turn in the α-helix?

A

3.6, the amino acid will hydrogen bond with the amino acid 3.6 residues away.

40
Q

How did Linus Pauling figure out the secondary structure of proteins?

A

He considered:

A) The planar amide bond

B) The rotation around the other two bonds

C) The recent 3D structures that had been described

41
Q

How do the termini of the amino acid chains allign in a β sheet?

A

One runs C to N while the other runs anti-parallel N to C.

42
Q

Name the five interactions that stablise proteins.

A
  1. Hydrogen bonding
  2. Hydrophobic (side chain) interactions
  3. Electrostatic (side chain) interactions
  4. Metal ion coordination
  5. Disulfide bond formation
43
Q

What is the requirement for forming disulfide bridges? What amino acid contains the thiol that takes part?

A

Oxidising conditions meaning they only form in extracellular proteins as cells have reducing conditions. Cystine.

44
Q

Name five post translational modifications possible to do to proteins.

A
  • Phosphorylation
  • Glycosylation (attach sugars)
  • Acylation
  • Alkylation
  • Addition of other protiens
45
Q

How does nature turn its enzymes on and off?

A

Reversible protein phosphorylation, attaching a PO4 group. This is a key anti-cancer target for drugs.

46
Q

What are enzymes extremely specific?

A

Operate in mild conditions, have extreme catalytic power and have absolute specifity.

47
Q

How many times does glycoside increase the rate of cleaving the ester linkage of celluose?

A

1018 times

48
Q

How are enzymes specific to the desired substrate?

A

They use indentations, grooves and pockets on the enzyme surface as well as all non-covalent interactions to have very strong attractions to a specific substrate.

49
Q

What are the five main ways catalysts can increase the rate of a reaction?

A
  1. Proximity and orientation
  2. Covalent catalysis
  3. Acid/Base catalysis
  4. Electrostatics
  5. Strain
50
Q

Describe how proximity and orientation can be used to increase rates of catalysis.

A

By holding groups together, the effective concentration can increase to extremely large values meaning even slow reactions become very fast.

To react, the correct orientation of the substrates must be adopted. Using all non-covalent interactions, the enzyme holds the substrate in the correct orientation.

51
Q

Describe how enzymes use covalent (nucleophilic) catalysis.

A

The enzyme forms covalent bonds with the substrate which create a stabilised intermediate. Common nucleophiles are S- from cysteine and COO- groups from aspartate and glutamate.

52
Q

What is natures primary amine?

A

Lysine, it has very important reactvity using amine chemistry in many parts of the body.

53
Q

Describe how enzymes uses general acid/base properties in catalysis.

A

Having a source of acid directly next to the reacting group will vastly speed up the rate that acid catalysis will occur. Having basic residues nearby is a huge benefit as well as acid and base catalysis can occur simaltaneously.

54
Q

What is the reactive structure and pKa of Asp/Glu?

A

COO-, pKa=4

55
Q

What is the reactive structure and pKa of His?

A

Imidazole, pKa=6

56
Q

What is the reactive structure and pKa of Cys?

A

Thiol, pKa=8

57
Q

What is the reactive structure and pKa of Lys?

A

-NH3+, pKa=9.5

58
Q

What is the reactive structure and pKa of Ser/Thr?

A

-OH, pka=14

59
Q

Describe how enzymes use electrostatics in catalysis.

A

Using charged groups on the enzyme, transistion state charges can be stablised before they even form, favouring the transition state formation. This can be perfomed by metal ions. This is useful for enol favouring of reactants.

60
Q

How do enzymes use strain in catalysis?

A

The enzyme distorts the shape of the substrates into more reactive conformations.

61
Q

What evidence is there for the fact enzymes stabilise the transition state?

A

Transition state mimics inhibit enzyme activity. Catalytic enzymes have been developed called abzymes which bind strongly to transition state mimics.

62
Q

How do the 20 natural amino acids perform functions that they wouldn’t usually be able to do?

A

They use metals and co-factors (often from vitamins).

63
Q

What is natures hydride source?

A

NADH

64
Q

What is another name for Lysozyme and what is it’s function?

A

HEWL (Hen egg white lysozyme) is an enzyme found in tears and egg whites. It catalyses the breakdown of bacterial cell walls called acetal hydrolysis.

65
Q

What is the mechanistic action of HEWL?

A
66
Q

Describe how pH and chain length affect the rate of lysozymes catalysis.

A

The reacting groups from the enzyme are pH dependant and above pH 6 and below pH 4 they won’t be in the correct form to react, meaning the rate drops. pH 5 is the maximum rate.

Rates increase until 6 sugar units have been reached. After that the rate does not change.

67
Q

Where specifically does lysozyme act?

A

Lysozyme cleaves the bond between the 4th and 5th sugars.

68
Q

What features does the transition state of the sugar being cleaved by lysozyme have and how is this used in medicine?

A

The carbon 1 position has a partial positive charge and is sp2 hybridised. Drugs can mimic this with a carbonyl at the carbon 1 postion. This binds stronger than the substrate.

69
Q

Define the turnover number.

A

Turnover number, kcat, is the number of substrate molecules that can be converted to a product by 1 enzyme molecule in 1 second.

70
Q

Define Km.

What do high and low values mean?

A

The [S] that gives kmax/2

High values give a low affinity for the substrate, low values mean there is a high affinity.

71
Q

Define kcat and the specificty constant.

A

kcat=Vmax/[E]total

Specifity constant=kcat/Km

72
Q

Name the two types and subcatagories of enzyme inhibition.

A
  1. Irreversible
  2. Reversable, competative and non competative
73
Q

How do irreversable inhibitors behave?

A

Usually form a covalent bond to the enzyme, often to a nucleophilic side chain. This permanently inactivates the enzyme as it blocks the active site.

74
Q

How do reversible competative inhibitors and non competative inhibitors act?

A

Competative bind to the active site as a substrate would by mimicing it or the transition state, this increases the concentration of S needed to reach Vmax.

Non-competative bind somewhere other than the active site and prevent the catalytic action. This lowers Vmax.

Chem@York Core 2&3 (13 decks)

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